Research Center for Agricultural Information Technology, NARO

Development of "Pedigree Finder", a web-based crop family tree creation tool

- Database that provides and utilizes information on ancestors & descendants of cultivars -

National Agriculture and Food Research Organization (NARO), in collaboration with Research Organization of Information and Systems (ROIS), has developed a database "Pedigree Finder" that allows users to freely create a family tree (pedigree chart) of crops. This database has a user-friendly interface to display a pedigree chart including cultivars and lines of interest in a visible format. Crop characteristics they exhibit can also be indicated. Therefore, breeders can use this to efficiently select the optimal combination of parents for breeding cultivars with desired traits. In addition, since it can be used in the same way for multiple crop species, it is expected to be widely used as a tool for pedigree information utilization, such as for agricultural producers and consumers to understand the characteristics of cultivars.


Overview

In order to respond to the increasing global demand for food, the strengthening of food security measures, and the intensifying climate change, etc., there is a constant need to develop new cultivars. In order to meet this social demand, it is necessary to accelerate and improve the efficiency of the process of breeding new varieties, which involves crossing existing varieties and lines, producing a variety of lines (candidate varieties), properly evaluating the traits of each line and selecting superior lines that will become the next-generation cultivars.

However, useful information for breeding, including pedigree, trait, genetic information, etc., is scattered among research institutes and crops. Also, since the data format of this breeding information is not uniform, it has been difficult to quickly determine the optimal combination at the stage of selecting the existing cultivars for the first cross.

Therefore, NARO and ROIS have developed a database "Pedigree Finder" that enables anyone to utilize crop pedigree information easily. "Pedigree Finder" centrally manages pedigree information of various crops such as rice and strawberries on the web. In addition, we have realized to provide the pedigree information and characteristics of cultivars as a database that can be viewed visually. Within the scope of data usage rights for each user, pedigree information maintained across crops and information on characteristics such as cultivars can be used freely according to the purpose.

The usage of "Pedigree Finder" is not limited to situations where breeders select mating parents considering close relationships, but also it is used in the case where the researchers elucidate "genetic factors" that are inherited from parents to offspring from the perspective of molecular breeding, and in the case where agricultural producers select cultivars based on characteristics. This database has completed its trial operation and will start full-scale operation for the domestic market with five types of crops (rice, strawberry, wheat, sweet potato, and red bean).
URL: Pedigree Finder Top Page(https://pedigree.db.naro.go.jp/)(Japanese only)


Publication

Pedigree Finder: A web-based crop pedigree viewer for graph databases
Hiromi Kajiya-Kanegae, Kei Matsushita, Takeshi Hayashi, Shuichi Kawashima, Akitoshi Goto, Akane Takezaki, Masahiro Yano, Genichiro Kikui, Jun-Ichi Yonemaru. Breeding Research (2022)24:115-123 URL: https://www.jstage.jst.go.jp/article/jsbbr/24/2/24_22J02/_article/-char/en


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